Integration of VarSome API in an existing bioinformatic pipeline for automated ACMG interpretation of clinical variants.

OBJECTIVE: While the bioinformatic workflow, from quality control to annotation, is quite standardized, the interpretation of variants is still a challenge. The decreasing cost of massively parallel NGS has produced hundreds of variants per patient to analyze and interpret. The ACMG "Standards and guidelines for the interpretation of sequence variants", widely adopted in clinical settings, assume that the clinician has a comprehensive knowledge of the literature and the disease. MATERIALS AND METHODS: To semi-automatize the application of the guidelines, we decided to develop an algorithm that exploits VarSome, a widely used platform that interprets variants on the basis of information from more than 70 genome databases. RESULTS: Here we explain how we integrated VarSome API into our existing clinical diagnostic pipeline for NGS data to obtain validated reproducible results as indicated by accuracy, sensitivity and specificity. CONCLUSIONS: We validated the automated pipeline to be sure that it was doing what we expected. We obtained 100% sensitivity, specificity and accuracy, confirming that it was suitable for use in a diagnostic setting.

CNV analysis in a diagnostic setting using target panel.

OBJECTIVE: Copy-number variation (CNV) is an important source of genetic diversity in humans. It can cause Mendelian or sporadic traits or be associated with complex diseases by various molecular mechanisms, including gene dosage, gene disruption, gene fusion and position effects. In clinical diagnostics, it is therefore fundamental to be able to identify such variations. The preferred techniques for CNV detection are MLPA, aCGH and qPCR, which have proven to be valuable, and they are complex, costly and require prior knowledge of the region to analyze. CNV calling from NGS data still suffers from data variability. Coverage can vary greatly from one region of the genome to another, depending on many factors like complexity, GC content, repeated regions and many others. In this paper, we describe how we developed a method for CNV detection. MATERIALS AND METHODS: Our method exploits CoNVaDING to detect single- and multiple-exon CNVs in targeted NGS data. RESULTS: We demonstrated that our CNV analysis has 100% specificity and 99.998% sensitivity. We also show how we evaluated the performance of this method based on internal analysis. CONCLUSIONS: The results indicate that the method can be used to screen prior to standard labs technologies, thus reducing the number of analyses, as well as costs, and increasing test conclusiveness.

Genetics of fat deposition.

Adipose tissue distribution usually varies among men and women. In men, adipose tissue is known to accumulate in the abdominal region surrounding the visceral organs (android fat distribution) whereas, in women, the accumulation of adipose tissue generally occurs in the gluteal-femoral regions (gynoid fat distribution). In some cases, however, android distribution can be found in women and gynoid distribution can be found in men. The regulation of adipose tissue accumulation involves interaction of a variety of genetic and environmental factors. This review examines genetic factors that cause differential distribution of adipose tissue in different depots of the body, between men and women and between different ethnicities. Genome-wide association studies can be used to identify genetic associations with the distribution and accumulation of adipose tissue. Insight into adipose tissue accumulation and distribution mechanisms could lead to development of personalized interventions for people who develop increased fat mass.

Steroid-converting enzymes in human adipose tissues and fat deposition with a focus on AKR1C enzymes.

Adipocytes express various enzymes, such as aldo-keto reductases (AKR1C), 11ß-hydroxysteroid dehydrogenase (11ß-HSD), aromatase, 5α-reductases, 3ß-HSD, and 17ß-HSDs involved in steroid hormone metabolism in adipose tissues. Increased activity of AKR1C enzymes and their expression in mature adipocytes might indicate the association of these enzymes with subcutaneous adipose tissue deposition. The inactivation of androgens by AKR1C enzymes increases adipogenesis and fat mass, particularly subcutaneous fat. AKR1C also causes reduction of estrone, a weak estrogen, to produce 17ß-estradiol, a potent estrogen and, in addition, it plays a role in progesterone metabolism. Functional impairments of adipose tissue and imbalance of steroid biosynthesis could lead to metabolic disturbances. In this review, we will focus on the enzymes involved in steroid metabolism and fat tissue deposition.

Improvement of quality of life by intake of hydroxytyrosol in patients with lymphedema and association of lymphedema genes with obesity.

OBJECTIVE: Lymphedema is a debilitating disease and may be a comorbidity of obesity. New molecules have been investigated for the treatment of lymphedema; one of the most promising molecules is hydroxytyrosol. The aim of this study was to evaluate the association between mutations in genes mutated in lymphedema and the presence of obesity and making an estimate of the quality of life in lymphedema patients. MATERIALS AND METHODS: We recruited 71 Caucasian individuals with the diagnosis of primary lymphedema, and they undertook a questionnaire to assess their quality life. For this purpose, we developed a NGS custom-made panel comprising genes associated with lymphedema. RESULTS: An obesity rate of 20% was detected. The average Lymph-ICF-LL value for patients who consume olive oil daily was 20 with a better quality of life. Twenty-three patients resulted positive to the genetic test. Genetic variants with a likely association with obesity have been identified in PROX1, FOXC2 and FLT4. CONCLUSIONS: A obesity rate, higher than that reported by ISTAT, was detected. The use of olive oil enhances the quality of life of lymphedema patients. Moreover, a diagnostic approach by a NGS panel shows an association of lymphedema with obesity.

Study of the effects of Lemna minor extracts on human immune cell populations.

OBJECTIVE: Lemna minor is a plant with a huge repertoire of secondary metabolites. The literature indicates that extracts of Lemna minor have antioxidant, antiradical, immunomodulatory and anti-inflammatory properties. The objective of the present study was to find a suitable technique to extract active compounds from this plant and verify whether these extracts have immunomodulatory activity. MATERIALS AND METHODS: We grew L. minor on a standard medium with Gamborg B5 and vitamins. We extracted compounds from the plant by maceration and decoction. The phytochemical profile of the extracts was characterized by chromatography, spectrophotometry, and spectroscopy. The extracts were tested on cultures of mononuclear cells from four human subjects. These cells were pulsed with carboxyfluorescein succinimidyl ester, grown in triplicate in standard culture medium without (control) and with increasing concentrations of Lemna extracts. Flow cytometry was used to evaluate cell death and proliferation of the total mononuclear cell population and of CD4+, CD8+, B cell and monocyte populations. RESULTS: The Lemna extracts were not cytotoxic and did not cause cell necrosis or apoptosis in immune cells. At low concentrations, they induced very limited proliferation of CD4+ cells within 48 hours. At high concentrations, they induced proliferation of CD8+ cells and B lymphocytes within 48 hours. CONCLUSIONS: Unfortunately, we failed to confirm any immunomodulatory activity of Lemna extracts. Growth and death rates of human immune cells were not significantly affected by adding Lemna extracts to the culture medium.

In vitro cell culture of amniotic fluid keratinocytes on amniotic membrane: the ideal tissue for repairing skin ulcers.

OBJECTIVE: The amniotic fluid contains a large population of stem keratinocytes demonstrating minimal immunological rejection. Recent evidence suggests that stem cells from the amniotic fluid can be employed in the field of tissue engineering. In this work we identified precursors of the epithelial cells and expanded them in vitro. MATERIALS AND METHODS: After collecting samples of amniotic fluid and separating the cells via centrifugation, we seeded a portion of these cells in selection media to analyze the proliferation of epithelial cells. The stem cells precursors of keratinocytes were identified through specific markers. The expression of these markers was evaluated by immunofluorescence and reverse transcription polymerase chain reaction (PCR). RESULTS: The stem cells demonstrated 90% confluence, after undergoing proliferation in the selection medium for 15 days. Most of these cells tested positive for the keratinocyte-specific markers, but negative for stem cell specific markers. Of note, the identity of the keratinocytes was well established even after several subcultures. CONCLUSIONS: These results suggested that it is feasible to isolate and expand differentiated cell populations in the amniotic fluid from precursor cells. Furthermore, amniotic membranes can be utilized as scaffolds to grow keratinocytes, which can be potentially exploited in areas of skin ulcer transplantation and tissue engineering interventions.

Effect of a dietary supplement on the reduction of lymphedema-progression in mouse tail-cut model.

OBJECTIVE: The aim of our study was to evaluate in vivo, in a mouse tail model of lymphedema, the effects of a dietary supplement, Garlive®, based on hydroxytyrosol from olive leaves, spermidine from rice seeds, hesperidin from citrus fruits and vitamin A. Hydroxytyrosol has anti-inflammatory, antioxidant and antimicrobial activities and inhibits leukotriene B4 generation; spermidine is able to inhibit the production of pro-inflammatory cytokines and mediators; hesperidin inhibits the secretion of pro-inflammatory cytokines: IFN-γ, IL-2, IL-4, IL-10; vitamin A deficiency was shown to induce inflammation and aggravate existing inflammatory states, whereas supplementation with vitamin A could ameliorate inflammation. MATERIALS AND METHODS: The active compounds were included in tablets: 250 mg of olive leaf extract titrated in 10% hydroxytyrosol, 200 mg of citrus fruits extract titrated in 60% hesperidin, 10 mg of rice (Oryza sativa) seeds extract titrated in 1% spermidine and 0.8 mg of vitamin A. Mice of an inbred group were randomly selected and divided in the control group and drug-treated group. The wound necessary for lymphedema generation was made on the tail of each mice 1 cm below the base of the trunk. RESULTS: After surgical intervention, there was a gradual increase in the circumference of both ends of the wound. The control group showed higher increase of tail volume than the drug-treated group. The differences in tail swelling between the control group and the drug-treated group were significantly different. The peak of swelling was anticipated to the 6th day in the drug-treated group, whereas in the control group the peak was reached later on. CONCLUSIONS: The tested drug prevented the induction of swelling from day 5th of wound creation and decreased the duration of swelling, favoring the wound healing.

Proposal of a food supplement for the management of post-COVID syndrome.

A vast majority of COVID-19 patients experience fatigue, extreme tiredness and symptoms that persist beyond the active phase of the disease. This condition is called post-COVID syndrome. The mechanisms by which the virus causes prolonged illness are still unclear. The aim of this review is to gather information regarding post-COVID syndrome so as to highlight its etiological basis and the nutritional regimes and supplements that can mitigate, alleviate or relieve the associated chronic fatigue, gastrointestinal disorders and continuing inflammatory reactions. Naturally-occurring food supplements, such as acetyl L-carnitine, hydroxytyrosol and vitamins B, C and D hold significant promise in the management of post-COVID syndrome. In this pilot observational study, we evaluated the effect of a food supplement containing hydroxytyrosol, acetyl L-carnitine and vitamins B, C and D in improving perceived fatigue in patients who recovered from COVID-19 but had post-COVID syndrome characterized by chronic fatigue. The results suggest that the food supplement could proceed to clinical trials of its efficacy in aiding the recovery of patients with long COVID.

Prevention of the proliferation of oral pathogens due to prolonged mask use based on α-cyclodextrin and hydroxytyrosol mouthwash.

OBJECTIVE: Face masks help contain the aerosol-mediated transmission of infectious viral particles released from individuals via cough and sneezes. However, the prolonged use of face masks has raised concerns regarding oral hygiene. Here, we present a mouthwash formulation based on α-cyclodextrin and hydroxytyrosol that can maintain healthy oral microbiota. MATERIALS AND METHODS: We isolated and cultured Candida albicans, Staphylococcus aureus, and a mix of Streptococcus sp., Staphylococcus sp. and Neisseria sp. from oral and throat swabs. The microorganisms were cultured in a standard medium with or without the mouthwash. To evaluate the effect of the mouthwash on the oral microbiota, the DNA from the saliva of 3 volunteers that used the mouthwash was extracted. Then, the DNA was amplified using primer pairs specific for bacterial and fungal DNA. Twelve further volunteers were offered to use the mouthwash and a questionnaire was submitted to them to assess the possible beneficial effects of mouthwash on halitosis and other oral disturbances. RESULTS: The bacteria and fungi cultured in media containing the mouthwash showed a growth reduction ranging from 20 to 80%. The PCR amplification of fungal and bacterial DNA extracted from volunteers that used the mouthwash showed a reduction of both bacteria and fungi. Volunteers that used the mouthwash reported a tendency towards a reduction of halitosis, gingival and mouth inflammation, and dry mouth. CONCLUSIONS: The use of a mouthwash containing α-cyclodextrin and hydroxytyrosol is not aggressive against oral mucosa; it is safe and effective to reduce the bacterial and fungal load due to the continuous use of face masks.

In vitro and clinical studies on the efficacy of α-cyclodextrin and hydroxytyrosol against SARS-CoV-2 infection.

OBJECTIVE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus responsible for the current pandemic of coronavirus disease 2019 (COVID-19). This virus attacks cells of the airway epithelium by binding transmembrane angiotensin-converting enzyme 2 (ACE2). Hydroxytyrosol has anti-viral properties. Alpha-cyclodextrin can deplete sphingolipids and phospholipids from cell membranes. The aim of the present experimental study was to evaluate the efficacy of α-cyclodextrin and hydroxytyrosol in improving defenses against SARS-CoV-2 infection in in vitro cell models and humans. PATIENTS AND METHODS: For in vitro experiments on Vero E6 cells, RNA for RT-qPCR analysis was extracted from Caco2 and human fibroblast cell lines. For study in humans, the treatment group consisted of 149 healthy volunteers in Northern Cyprus, considered at higher risk of SARS-CoV-2 infection than the general population. The volunteers used nasal spray containing α-cyclodextrin and hydroxytyrosol for 4 weeks. The control group consisted of 76 healthy volunteers who did not use the spray. RESULTS: RT-qPCR experiments on targeted genes involved in endocytosis showed a reduction in gene expression, whereas cytotoxicity and cytoprotective tests showed that the compounds exerted a protective effect against SARS-CoV-2 infection at non-cytotoxic concentrations. None of the volunteers became positive to SARS-CoV-2 RT-qPCR assay during the 30 days of treatment. CONCLUSIONS: Treatment with α-cyclodextrin and hydroxytyrosol nasal spray improved defenses against SARS-CoV-2 infection and reduced synthesis of viral particles.

Scoping review on the role and interactions of hydroxytyrosol and alpha-cyclodextrin in lipid-raft-mediated endocytosis of SARS-CoV-2 and bioinformatic molecular docking studies.

OBJECTIVE: The aim of the study was to show the effect that two naturally occurring compounds, a cyclodextrin and hydroxytyrosol, can have on the entry of SARS-CoV-2 into human cells. MATERIALS AND METHODS: The PubMed database was searched to retrieve studies published from 2000 to 2020, satisfying the inclusion criteria. The search keywords were: SARS-CoV, SARS-CoV-2, coronavirus, lipid raft, endocytosis, hydroxytyrosol, cyclodextrin. Modeling of alpha-cyclodextrin and hydroxytyrosol were done using UCSF Chimera 1.14. RESULTS: The search results indicated that cyclodextrins can reduce the efficiency of viral endocytosis and that hydroxytyrosol has antiviral properties. Bioinformatic docking studies showed that alpha-cyclodextrin and hydroxytyrosol, alone or in combination, interact with the viral spike protein and its host cell receptor ACE2, thereby potentially influencing the endocytosis process. CONCLUSIONS: Hydroxytyrosol and alpha-cyclodextrin can be useful against the spread of SARS-CoV-2.

Naturally-occurring and cultured bacteriophages in human therapy.

OBJECTIVE: The aim of the study was to show the importance of developing techniques that could exploit the potential of bacteriophages as therapeutics or food supplements. MATERIALS AND METHODS: PubMed database was searched using the following combination of keywords: (bacteriophage) AND (human therapy); (natural bacteriophage) AND (application). RESULTS: The increasing antibiotic resistance of many bacterial strains is making standard antibiotic treatments less effective. Phage therapy provides a non-antibiotic alternative with greater specificity and without harmful effects on the human microbiota. Phages target their specific bacteria, replicate, and then, destroy the host pathogen. Bacteriophages may be administered by several routes, including topical, oral and intravenous. They not only destroy the host pathogen but, in some cases, increase the sensitivity of host bacteria to antibiotics. Various studies have shown that combining phage therapy and antibiotic treatment can be effective against bacterial infections. Clinical trials of phage therapy have shown promising results for various human diseases and conditions. With advances in genetic engineering and molecular techniques, bacteriophages will be able to target a wide range of bacteria. CONCLUSIONS: In the future, phage therapy promises to become an effective therapeutic option for bacterial infections. Since many potentially beneficial bacteriophages can be found in food, supplements containing bacteriophages could be designed to remodel gut microbiota and eliminate pathogenic bacteria. Remodeling of gut microbiota could correct gut dysbiosis. The order of phages known to have these promising activities is Caudovirales, especially the families Siphoviridae and Myoviridae.

From Myo-inositol to D-chiro-inositol molecular pathways.

OBJECTIVE: Inositol is a carbocyclic sugar polyalcohol. By epimerization of its hydroxyl groups, nine possible stereoisomers can be generated, two of major physiological and clinical relevance: myo-inositol and D-chiro-inositol. Myo-inositol and D-chiro-inositol are normally stored in kidney, brain and liver and are necessary for functions, such as signal transduction, metabolic flux, insulin signaling, regulation of ion-channel permeability, stress response and embryo development. In this narrative review, we summarize the mechanisms by which myo-inositol and D-chiro-inositol can be synthesized and absorbed and their possible role in the etiopathogenesis of neural tube defects. MATERIALS AND METHODS: We performed an online search in the PubMed database using the following keywords: "inositol", "D-chiro-inositol", "myo-inositol", "neural tube defects and inositol". RESULTS: Inositol requirements are partly met by dietary intake, while the rest is synthesized endogenously. Inositol deficiency may be involved in the pathogenesis of diseases, such as metabolic syndrome, spina bifida (a neural tube defect), polycystic ovary syndrome and diabetes. Supplementation of the two inositol stereoisomers, D-chiro-inositol and myo-inositol is important to prevent these conditions. CONCLUSIONS: Inositol is fundamental for signal transduction in the brain, kidneys, reproductive organs and other tissues in response to neurotransmitters, hormones and growth factors. Various genes are involved in inositol metabolism and associated pathways. Altered inositol concentrations are observed in several diseases. Analysis of the genes involved in inositol metabolism may provide important information for the clinical management of these conditions.

Pheromone receptors and their putative ligands: possible role in humans.

Pheromones are ectohormones that play an important role in communication and behavior. Pheromones and pheromone receptor genes are important in mice and other mammals that rely heavily on pheromone cues to survive. Although there is controversy about whether pheromones and pheromone receptor genes have the same importance or are even active in humans, there are some hints that they might have roles in sociosexual behavior and mental disorders. The aim of this qualitative review was to provide an overview of the state of the art regarding pheromones and pheromone receptors in humans and their possible implications in human physiology and pathology. An electronic search was conducted in MEDLINE, PubMed and Scopus databases for articles published in English up to December 2018. The search concerned a possible role of pheromones and pheromone receptors in humans with implications for sociosexual behavior, mental disorders, the menstrual cycle and nutrition. Pheromone communication in humans has not been definitively demonstrated. However, the potential ability of putative pheromones to activate the hypothalamus, which controls the release of many hormones, suggests they could have a role in systemic functions in humans. Future confirmation of the effects of pheromones and pheromone receptors in humans could be useful in the prevention and treatment of various human disorders.

Putative role of Brugada syndrome genes in familial atrial fibrillation.

OBJECTIVE: Familial atrial fibrillation (FAF), a not uncommon arrhythmia of the atrium, is characterized by heritability, early onset and absence of other heart defects. The molecular and genetic basis is still not completely clear and genetic diagnosis cannot be achieved in about 90% of patients. In this study, we present the results of genetic screening by next generation sequencing in affected Russian families. PATIENTS AND METHODS: Sixty subjects (18 probands and 42 relatives) with a clinical diagnosis of FAF were enrolled in the study. Since AF frequently associates with other cardiomyopathies, we included all genes that were known to be associated with these disorders at the time of our study. All probands were therefore systematically screened for 47 genes selected from the literature. RESULTS: Our study revealed that seven variants co-segregated with the clinical phenotype in seven families. Interestingly, four out of six genes and three out of seven variants have already been associated with Brugada syndrome in the literature. CONCLUSIONS: To our knowledge, this is the first report of association of the CACNA1C, CTNNA3, PKP2, ANK2 and SCN10A genes with FAF; it is also the first study in Russian families.

Genetics of lipedema: new perspectives on genetic research and molecular diagnoses.

OBJECTIVE: The aim of this qualitative review is to provide an update on the current understanding of the genetic determinants of lipedema and to develop a genetic test to differentiate lipedema from other diagnoses. MATERIALS AND METHODS: An electronic search was conducted in MEDLINE, PubMed, and Scopus for articles published in English up to March 2019. Lipedema and similar disorders included in the differential diagnosis of lipedema were searched in the clinical synopsis section of OMIM, in GeneCards, Orphanet, and MalaCards. RESULTS: The search identified several genetic factors related to the onset of lipedema and highlighted the utility of developing genetic diagnostic testing to help differentiate lipedema from other diagnoses. CONCLUSIONS: No genetic tests or guidelines for molecular diagnosis of lipedema are currently available, despite the fact that genetic testing is fundamental for the differential diagnosis of lipedema against Mendelian genetic obesity, primary lymphedema, and lipodystrophies.

Mendelian obesity, molecular pathways and pharmacological therapies: a review.

OBJECTIVE: In this qualitative review we analyze the major pathways and mechanisms involved in the onset of genetically-determined obesity (Mendelian obesity), identifying possible pharmacological treatments and trials. MATERIALS AND METHODS: We searched PubMed with the keywords (obesity[Title/Abstract]) AND mutation[Title/Abstract], and OMIM with the keyword "obesity". In both cases, we selected non-syndromic Mendelian obesity. We then searched ClinicalTrials.gov with the following criteria: "recruitment status: active, not recruiting and completed"; "study type: interventional (clinical trial)"; "study results: with results"; type of intervention: "drug or dietary supplement". RESULTS: From the PubMed and OMIM searches we obtained a total of 15 genes associated with monogenic Mendelian obesity. From ClinicalTrials.gov we retrieved 46 completed or active trials of pharmacological treatments. CONCLUSIONS: We summarized the molecular bases of Mendelian obesity and searched for any clinical trials completed or underway for the treatment of severe forms of obesity. Most Mendelian obesities are linked to dysfunctions in the leptin/melanocortin signaling pathway, and most of the possible drugs target this pathway in order to improve energy expenditure and reduce food intake.

Taste, olfactory and texture related genes and food choices: implications on health status.

OBJECTIVE: The food choices are due to a mixture of sensory signals including gustatory, olfactory, and texture sensations. The aim of this quality review was to update data about studies concerning genetics of taste, olfactory and texture receptors and their influence on the health status in humans. MATERIALS AND METHODS: An electronic search was conducted in MEDLINE, Pubmed database and Scopus, for articles published in English until December 2018. Two independent researches selected the studies and extracted the data. RESULTS: The review confirms the importance of inter-individual variations in taste, olfactory and texture related genes on food choices and their implications in the susceptibility to nutrition-related conditions such as obesity, dental caries, diabetes, cardiovascular disease, hypertension, hyperlipidemia and cancer. CONCLUSIONS: The knowledge of variants in taste, olfactory and texture related genes can contribute to the prevention of diseases related to unhealthy nutrition. Further studies would be useful to identify other variants in the genes involved in these systems.